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- PDB-7uft: Cryo-EM Structure of Bl_Man38C at 2.9 A -

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Basic information

Entry
Database: PDB / ID: 7uft
TitleCryo-EM Structure of Bl_Man38C at 2.9 A
ComponentsAlpha-mannosidase
KeywordsHYDROLASE / n-glycan / probiotic / a-mannosidase / gh38
Function / homology
Function and homology information


alpha-mannosidase activity / mannose metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain ...Glycosyl hydrolases family 38, C-terminal beta sandwich domain / Glycosyl hydrolases family 38 C-terminal beta sandwich domain / Glycoside hydrolase family 38, N-terminal domain / Glycosyl hydrolase family 38, C-terminal / Glycoside hydrolase family 38, central domain / Glycoside hydrolase family 38, central domain superfamily / Glycosyl hydrolases family 38 N-terminal domain / Glycosyl hydrolases family 38 C-terminal domain / Alpha mannosidase middle domain / Alpha mannosidase, middle domain / Glycoside hydrolase 38, N-terminal domain superfamily / Glycoside hydrolase families 57/38, central domain superfamily / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Galactose mutarotase-like domain superfamily
Similarity search - Domain/homology
Biological speciesBifidobacterium longum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSantos, C.R. / Cordeiro, R.L. / Domingues, M.N. / Borges, A.C. / de Farias, M.A. / Van Heel, M. / Murakami, M.T. / Portugal, R.V.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2015/26982-0 Brazil
Sao Paulo Research Foundation (FAPESP)2017/15340-2 Brazil
CitationJournal: Nat.Chem.Biol. / Year: 2022
Title: Cryo-EM Structure of Bl_Man38C at 2.9 A
Authors: Santos, C.R. / Cordeiro, R.L. / Domingues, M.N. / Borges, A.C. / de Farias, M.A. / Van Heel, M. / Murakami, M.T. / Portugal, R.V.
History
DepositionMar 23, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-mannosidase
B: Alpha-mannosidase
C: Alpha-mannosidase
D: Alpha-mannosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,8698
Polymers470,6074
Non-polymers2624
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Alpha-mannosidase


Mass: 117651.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium longum (bacteria) / Strain: NCC 2705 / Gene: BL1329 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8G4P9
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Tetramer of Bl_Man38C / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.470 MDa / Experimental value: NO
Source (natural)Organism: Bifidobacterium longum (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
Details: 150 mM sodium chloride, 20 mM sodium phosphate, pH 7.5
SpecimenConc.: 0.34 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm / Cs: 0.01 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 1.5 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3549: / Classification: refinement
EM software
IDNameCategory
1cisTEMparticle selection
2EPUimage acquisition
4cisTEMCTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10cisTEMinitial Euler assignment
11cisTEMfinal Euler assignment
13cisTEM3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56677 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00733120
ELECTRON MICROSCOPYf_angle_d0.65245020
ELECTRON MICROSCOPYf_dihedral_angle_d5.7119756
ELECTRON MICROSCOPYf_chiral_restr0.0494856
ELECTRON MICROSCOPYf_plane_restr0.0055900

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